Pirates and Ninjas are equally matched in terms of prowess, so the decision must come down to what it always comes down to in the end:
Who parties better?
The answer is cleary pirates. Pirates would throw the best parties ever. People would be dying and you'd be drunk off your ass and you'd be like "Oh fuck I'm going to die" but you'd be too pissed to care and you'd just be laughing, and you'd wake up in the morning and there'd be a peg leg in your ass and you'd be 2 months into a sea voyage and you were on dry land when you went to bed, and you'd just be so fucking glad to be alive.
That wouldn't happen with Ninjas.

If we're talking about martial prowess, I'm pretty sure a single ninja would burn though a pirate crew like a buzzsaw through a side of veal. I just prefer the pirate aesthetic._________________"Whatever afflicts thee, their asses I shall kick"